Hi,
If you are using the triple trajectory approach, the flags for the ligand
are *-yl* {ligand solvated traj} and *-slp* {ligand solvated prmtop}.
Regards,
Dwight
On Wed, Oct 21, 2015 at 11:19 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m trying to compare the delta-G of binding of a complex using the
> single- and three-trajectory approach.
>
> In the single trajectory approach, as per manual, th command used was:
>
> mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -sp cmplx_solv.prmtop -cp cmplx.prmtop -rp rec.prmtop -lp lig.prmtop -y *.nc
>
> To get a more accurate estimate of the desolation parts of the energy of
> the receptor and ligand, I’m trying to use the three trajectory approach. I
> have run separate trajectories of the complex and one of the subunits.
>
> I looked at the manual but could not find an appropriate flag for the
> solvated ligand file.
>
> I’d be grateful for any advice on the correct usage.
>
> Regards
>
> George
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--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Oct 21 2015 - 09:00:03 PDT
